ClinVar Miner

Submissions for variant NM_002769.5(PRSS1):c.508A>G (p.Lys170Glu)

gnomAD frequency: 0.00006  dbSNP: rs201550522
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000611439 SCV001000056 likely benign Hereditary pancreatitis 2023-11-13 criteria provided, single submitter clinical testing
Ambry Genetics RCV000611439 SCV001185412 benign Hereditary pancreatitis 2015-01-07 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001174692 SCV001337944 likely benign not specified 2021-01-19 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000611439 SCV002534764 benign Hereditary pancreatitis 2019-12-09 criteria provided, single submitter curation
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000611439 SCV004562804 uncertain significance Hereditary pancreatitis 2023-08-07 criteria provided, single submitter clinical testing The PRSS1 c.508A>G; p.Lys170Glu variant (rs201550522) is reported in one patient of Indian heritage with a clinical diagnosis of hereditary pancreatitis (Rebours 2009); and in two individuals with tropical calcific pancreatitis (TCP; Paliwal 2016). In addition, a single functional study on p.Lys170Glu showed approximately a 30 percent increased trypsinogen secretion and enzyme activity level (Schnur 2014), suggesting that this variant is likely to confer an increased risk for pancreatitis. This variant is also reported in ClinVar (Variation ID: 518381). It is observed in the general population with an overall allele frequency of 0.03% (49/152158 alleles, including 2 homozygotes) in the Genome Aggregation Database (gnomAD v3.1.2). Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.284). Based on the available information, the clinical significance of this variant is uncertain at this time. References: Paliwal S et al. Association Analysis of PRSS1-PRSS2 and CLDN2-MORC4 Variants in Nonalcoholic Chronic Pancreatitis Using Tropical Calcific Pancreatitis as Model. Pancreas. 2016 Sep;45(8):1153-7. PMID: 26784911. Rebours V et al. The natural history of hereditary pancreatitis: a national series. Gut. 2009 Jan;58(1):97-103. PMID: 18755888. Schnur A et al. Functional effects of 13 rare PRSS1 variants presumed to cause chronic pancreatitis. Gut. 2014 Feb;63(2):337-43. PMID: 23455445.

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